Re: [Jmol-users] An Old Paper and Jmol/Resolver

[Robert H. <ha...@st...>]

Great --

-- I suggest a "put it back together" link.

On Wed, Apr 13, 2011 at 12:28 PM, Otis Rothenberger
<osr...@ch...>wrote:

> Bob,
>
> I put a Google Standard InChI search link on my IL State Fair ACS kiosk toy
> suggestion:
>
> http://chemagic.com/web_molecules/acs.aspx
>
> Users can play with it to see what they think about the Google search
> approach. I hope the toy instructions are fairly intuitive. Here's my point
> of view and some specific notes relate the Google search:
>
> My View:
> I'm interested in developing more high school teacher interest in Jmol. To
> this end, I'm hoping to do some local section ACS speaking in the near
> future. I think any useful student utility that helps break an
> understandable mind set that Jmol is simply a "see the pretty molecule spin"
> application is a useful addition. I say understandable because "Jmol 2011"
> is really not that well known outside a small circle of users.
>
> Notes:
> 1) Google has obviously put some specific thought into chemical searching
> via InChI - some specifics below.
> 2) For some reason, Resolver has some problems with the cyclooctatetraene
> InChI. I suspect this is related to flat (aromatic) vs tub (not aromatic)
> confusion in the SMILES. Without putting up a "did you mean" warning, Google
> appends the search URL InCHI to improve the search.
> 3) Taxol seems to be big test compound with this toy, so I'll make a
> special Taxol note here. Resolver has some issues with % in some SMILES.


I don't think so. Must be your escaping. This works just fine in Jmol:

load $taxol
x = {*}.find("SMILES")
load smiles @x



> I have not been able to work this all out, but I suspect it's a query
> string issue with the percent sign location in certain SMILES. I've tried
> escaping the % sign itself with little success. I dodge this issue by
> trapping Jmol SMILES that have a %. I then have JME read the Jmol molfile,
> and I use the JME SMILES for this molfile. This, of course, produces the
> non-isomeric SMILES. I'd trap only problem SMILES if I could figure out the
> specific nature of this % sign problem. Back to Google: The search works.
> Google has obviously done a thorough job of indexing InChI's.
>

I note that "cholesterol" also picks up a related isomer, lathosterol, in a
Google search.


> Just to test pushing Jmol Script's ability to make these loading queries, I
> added a feature that will select PubChem's 2D sdf file if the 3D sdf is not
> available. Taxol is just such a model.


?? the 3D mol file of taxol is available. What's the issue?



>
> Otis
>
> --
> Otis Rothenberger
> Department of Chemistry
> Illinois State University Normal, IL 61790-4160
> http://chemagic.org
>
> ------------------------------
> *From*: "Robert Hanson" <ha...@st...>
> *Sent*: Wednesday, April 13, 2011 6:22 AM
> *To*: osr...@ch..., jmo...@li...
> *Subject*: Re: [Jmol-users] An Old Paper and Jmol/Resolver
>
>
> Otis, are you  suggesting we add a "Google" menu item in Jmol?
>
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>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900